/trunk Developers: mandevsgill

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mandevsgill 2013-05-16 07:51 Rev.: 5653

A few more minor changes (essentially all operations involving meanCache and storedMeanCache now done by cacheHelper). Rewritten code does not break anything.

0 lines of code changed in 2 files:

• src/dr/evomodel/continuous: IntegratedMultivariateTraitLikelihood.java (new)

mandevsgill 2013-05-14 17:55 Rev.: 5649

Some very minor changes

160 lines of code changed in 1 file:

• src/dr/evomodel/continuous: IntegratedMultivariateTraitLikelihood.java (+160 -10)

mandevsgill 2013-05-11 05:09 Rev.: 5645

Starting on diffusion with drift

5 lines of code changed in 2 files:

• src/dr/evomodel/continuous: AbstractMultivariateTraitLikelihood.java (new)

mandevsgill 2012-05-11 07:21 Rev.: 4948

Correct version of GMRF multilocus likelihood

268 lines of code changed in 1 file:

• src/dr/evomodel/coalescent: GMRFMultilocusSkyrideLikelihood.java (+268 -287)

mandevsgill 2011-10-21 07:40 Rev.: 4370

Latest version of GMRFMultilocusSkyrideLikelihood. Needs to be cleaned up.

17 lines of code changed in 1 file:

• src/dr/evomodel/coalescent: GMRFMultilocusSkyrideLikelihood.java (+17 -13)

mandevsgill 2011-10-13 15:16 Rev.: 4357

Updated the multilocus gmrf model so that we have a proper prior. Still needs to be cleaned up a little bit.

265 lines of code changed in 2 files:

• src/dr/evomodel/coalescent: GMRFMultilocusSkyrideLikelihood.java (+253 -4)
• src/dr/evomodelxml/coalescent: GMRFSkyrideLikelihoodParser.java (+12 -2)

mandevsgill 2011-09-13 05:35 Rev.: 4307

Latest version of GMRFMultilocusSkyrideLikelihood.

125 lines of code changed in 1 file:

• src/dr/evomodel/coalescent: GMRFMultilocusSkyrideLikelihood.java (+125 -105)

mandevsgill 2011-07-01 12:09 Rev.: 4087

Now the multilocus Skyride model should work.

5 lines of code changed in 3 files:

• src/dr/evomodel/coalescent: GMRFMultilocusSkyrideLikelihood.java (+5 -5)
• src/dr/evomodel/coalescent/operators: GMRFMultilocusSkyrideBlockUpdateOperator.java (-3)

mandevsgill 2011-07-01 10:39 Rev.: 4086

Multilocus GMRF model has been updated and appears to be working properly. Old GMRF model should still work with the old xml syntax.

832 lines of code changed in 6 files:

• src/dr/evomodel/coalescent: GMRFMultilocusSkyrideLikelihood.java (+405 -195), GMRFSkyrideLikelihood.java (+6 -2)
• src/dr/evomodel/coalescent/operators: GMRFMultilocusSkyrideBlockUpdateOperator.java (+377), GMRFMultiocusSkyrideBlockUpdateOperator.java (del)
• src/dr/evomodelxml/coalescent: GMRFSkyrideLikelihoodParser.java (+32 -5)
• src/dr/evomodelxml/coalescent/operators: GMRFSkyrideBlockUpdateOperatorParser.java (+12 -11)

mandevsgill 2011-01-30 12:17 Rev.: 3781

Modified precision in smoothing prior for multilocus case.

100 lines of code changed in 1 file:

• src/dr/evomodel/coalescent: GMRFMultilocusSkyrideLikelihood.java (+100 -6)

mandevsgill 2010-08-31 08:06 Rev.: 3473

GMRFMultilocusSkyrideLikelihood has been cleaned up and appears to work properly.

1 lines of code changed in 2 files:

• src/dr/evomodel/coalescent: GMRFMultilocusSkyrideLikelihood.java (+1 -1), GMRFSkyrideLikelihood.java (-1)

mandevsgill 2010-08-26 11:29 Rev.: 3449

Cleaned-up version of GMRFMultilocusSkyrideLikelihood. It appears to be working with the block update sampler.

58 lines of code changed in 3 files:

• src/dr/evomodel/coalescent: GMRFMultilocusSkyrideLikelihood.java (+47 -150), GMRFSkyrideLikelihood.java (+5 -4)
• src/dr/evomodel/coalescent/operators: GMRFMultiocusSkyrideBlockUpdateOperator.java (new 6)

mandevsgill 2010-08-25 05:21 Rev.: 3436

GMRF multilocus likelihood appears to compute properly; operators still do not work and there is debugging material to remove.

742 lines of code changed in 4 files:

• src/dr/evolution/coalescent: TreeIntervals.java (+3 -1)
• src/dr/evomodel/coalescent: GMRFMultilocusSkyrideLikelihood.java (+307 -66)
• src/dr/evomodel/coalescent/operators: GMRFMultiocusSkyrideBlockUpdateOperator.java (+422)
• src/dr/evomodelxml/coalescent/operators: GMRFSkyrideBlockUpdateOperatorParser.java (+10)

mandevsgill 2010-08-13 11:53 Rev.: 3387

Testing SVN

0 lines of code changed in 1 file:

• src/dr/evomodel/coalescent: GMRFMultilocusSkyrideLikelihood.java (-2)